THE HAGUE (AP) — The International Criminal Court acquitted a Congolese militia leader Tuesday of all charges of commanding fighters who destroyed a village in eastern Congo in 2003, raping and hacking to death some 200 people, including children.

The acquittal of Mathieu Ngudjolo on charges including rape, murder and pillage was only the second verdict in the court’s 10-year history and the first time it has cleared a suspect.

The only other ICC verdict, handed down earlier this year, convicted another Congolese rebel leader, Thomas Lubanga, of using child soldiers in battles in Ituri. He was sentenced to 14 years in prison.

The court has indicted far more senior suspects than Mr. Ngudjolo, including Sudanese President Omar al-Bashir and former Ivory Coast President Laurent Gbagbo. Mr. al-Bashir refuses to surrender to the court, and Mr. Gbagbo is in custody in The Hague awaiting a possible trial.

Tuesday’s verdict also cast a shadow over ICC prosecutors’ efforts to collect and present evidence of atrocities in complex conflicts thousands of miles from the court’s headquarters in The Hague.

Judges said the testimony of three key prosecution witnesses was unreliable and could not prove definitively that Mr. Ngudjolo led the rebel attack on the village of Bogoro, but they emphasized that Mr. Ngudjolo’s acquittal did not mean that no crimes occurred in the village.

“If an allegation has not been proven beyond a reasonable doubt … this does not necessarily mean that the alleged fact did not occur,” Presiding Judge Bruno Cotte of France said.

Mr. Ngudjolo showed no emotion at the acquittal. His lawyer, Jean-Pierre Kilenda, said his client had always insisted he was innocent.

Judges “showed that this court respects the rights of defendants,” the lawyer said.

Eric Witte, an expert in international law at the Open Society Justice Initiative, said the judgment “will send a worrying signal about the quality of ICC prosecutions.”

He said Prosecutor Fatou Bensouda now may need to rethink the way her office builds its cases.

“A pattern of prosecution failures could undermine support for the court as a whole,” Mr. Witte warned.

Prosecutors say many villagers in Bogoro were raped before some 200 were hacked to death with machetes by rebel fighters on a single day in February 2003.

Rights organizations immediately called upon the court to explain the acquittal to victims and survivors in the village in Congo’s eastern Ituri region, and to improve its investigations.

“The acquittal of Ngudjolo leaves the victims of Bogoro and other massacres by his forces without justice for their suffering,” said Geraldine Mattioli-Zeltner, international justice advocacy director at Human Rights Watch. “The ICC prosecutor needs to strengthen its investigations of those responsible for grave crimes in Ituri, including high-ranking officials in Congo, Rwanda and Uganda who supported the armed groups fighting there.”

Judges ordered Mr. Ngudjolo’s immediate release, but Ms. Bensouda said she would appeal the acquittals and asked for Mr. Ngudjolo to be kept in custody.

However, after a brief hearing later Tuesday, Judge Cotte again ordered him freed, saying that after an acquittal, “release should be more than ever the rule.”

It remained unclear exactly where Mr. Ngudjolo would go. Defense lawyer Jean-Pierre Fofe told the court that Mr. Ngudjolo most likely would stay in the Netherlands or in another European country pending the appeal.

Judges still are considering the evidence against another militia leader, Germain Katanga, who stood trial with Mr. Ngudjolo, and are expected to deliver that verdict next year.

Congo faces a myriad of rebel groups, including the emergence of one known as M23, sparking fighting that has forced hundreds of thousands to flee their homes in the country’s volatile east.

Kambasu Ngeve, M23’s chief negotiator in ongoing talks with the Congolese government, said he was delighted by Tuesday’s acquittal.

“I still thought that all those were brought to the ICC in the Ituri case were innocent and that the real culprits were free,” he told The Associated Press. “It doesn’t surprise me. I only regret that he spent a long time in prison.”

Congolese government spokesman Lambert Mende said “the government takes note of this decision, which we cannot interpret because it’s a judicial order and justice is independent.”

The ICC, the world’s first permanent war crimes tribunal, came into being in 2002, and the treaty that created it has been ratified by 121 nations. Prosecutors so far have indicted suspects in seven different countries, all of them in Africa, including Congo, Sudan, Kenya, Libya and Ivory Coast.